Fluorescence Signal Amplification Strategies Based on DNA Nanotechnology for miRNA Detection

In this review,the most recent progresses in the field of fluorescence signal amplification strategies based on DNA nanotechnology for miRNA are summarized.The types of signal amplification are given and the principles of amplification strategies are explained,including rolling circle amplification(RCA),catalytic hairpin assembly(CHA),hybridization chain reaction(HCR)and DNA walker.Subsequently,the application of these signal amplification methods in biosensing and bioimaging are covered and described.Finally,the challenges and the outlook of fluorescence signal amplification methods for miRNA detection are briefly commented.     

“发夹”结构DNA用于生物分析传感器研究进展

由于链内碱基互补配对作用形成的"发夹"结构DNA分子被广泛用于生物分子传感分析。双链或多链"发夹"结构DNA分子参与的杂交链式反应信号记录方式多样,主要有荧光法、比色法、电化学方法等。基于杂交链式反应的检测方法具有快速、方便、成本低、准确度高、灵敏度高、特异性强的优点,在分析传感研究中的应用尤其受到人们的关注,近些年发展迅速。本文综述了"发夹"结构DNA与杂交链式反应应用于生物传感分析的原理、信号记录方式及其在蛋白质、重金属离子、小分子、疾病标志物、DNA等检测中的研究进展。     

酶放大DNA电化学传感器的研究进展

DNA电化学传感器灵敏度高、选择性好、分析时间短和检测成本低,极大地推动了生物传感器的发展. 结合蛋白质酶、功能核酸酶的催化效率高与特异性好,可提高检测灵敏度和选择性. 本文评述了酶放大DNA电化学传感器的研究进展,并分析现存问题,展望发展趋势.     

Signal Amplification Technologies for the Detection of Nucleic Acids: from Cell-Free Analysis to Live-Cell Imaging

Due to their unique properties, such as programmability, ligand-binding capability, and flexibility, nucleic acids can serve as analytes and/or recognition elements for biosensing. To improve the sensitivity of nucleic acid-based biosensing and hence the detection of a few copies of target molecule, different modern amplification methodologies, namely target-and-signal-based amplification strategies, have already been developed. These recent signal amplification technologies, which are capable of amplifying the signal intensity without changing the targets’ copy number, have resulted in fast, reliable, and sensitive methods for nucleic acid detection. Working in cell-free settings, researchers have been able to optimize a variety of complex and quantitative methods suitable for deploying in live-cell conditions. In this study, a comprehensive review of the signal amplification technologies for the detection of nucleic acids is provided. We classify the signal amplification methodologies into enzymatic and non-enzymatic strategies with a primary focus on the methods that enable us to shift away from in vitro detecting to in vivo imaging. Finally, the future challenges and limitations of detection for cellular conditions are discussed.     

细胞内源性分子辅助荧光信号放大策略及细胞成像

细胞内原位信号放大策略是检测低丰度内源性目标物的有效手段, 但多数信号放大策略依赖于外源性辅助物, 不可避免地改变细胞内微环境, 进而对机体造成一定干扰. 针对此问题, 可利用细胞内源性物质(如金属离子、 核酸、 蛋白酶等)实现原位荧光信号放大, 对不同生物标志物进行荧光成像, 此方法对低丰度靶分子检测及成像具有重要意义. 本文对内源性物质辅助信号放大及细胞内荧光成像相关研究进行了归纳整理, 介绍了内源性核酸、 酶、 蛋白质、 三磷酸腺苷(ATP)和金属离子辅助信号放大策略, 并探讨了其信号放大机理; 总结了内源性物质辅助信号放大探针在低丰度物质检测及成像方面的研究进展; 最后展望了该策略在细胞成像方面的优势及应用前景.     

Sensitive electrochemical monitoring of nucleic acids coupling DNA nanostructures with hybridization chain reaction

Methods based on metal nanotags have been developed for metallobioassay of nucleic acids, but most involve complicated labeling or stripping procedures and are unsuitable for routine use. Herein, we report the proof-of-concept of a novel and label-free metallobioassay for ultrasensitive electronic determination of human immunodeficiency virus (HIV)-related gene fragments at an ultralow concentration based on target-triggered long-range self-assembled DNA nanostructures and DNA-based hybridization chain reaction (HCR). The signal is amplified by silver nanotags on the DNA duplex. The assay mainly consists of capture probe, detection probe, and two different DNA hairpins. In the presence of target DNA, the capture probe immobilized on the sensor sandwiches target DNA with the 3′ end of detection probe. Another exposed part of detection probe at the 5′ end opens two alternating DNA hairpins in turn, and propagates a chain reaction of hybridization events to form a nicked double-helix. Finally, numerous silver nanotags are immobilized onto the long-range DNA nanostructures, each of which produces a strong electronic signal within the applied potentials. Under optimal conditions, the target-triggered long-range DNA nanostructures present good electrochemical behaviors for the detection of HIV DNA at a concentration as low as 0.5 fM. Importantly, the outstanding sensitivity can make this approach a promising scheme for development of next-generation DNA sensors without the need of enzyme labeling or fluorophore labeling.     

Nucleic acid-based fluorescent probes and their analytical potential

It is well known that nucleic acids play an essential role in living organisms because they store and transmit genetic information and use that information to direct the synthesis of proteins. However, less is known about the ability of nucleic acids to bind specific ligands and the application of oligonucleotides as molecular probes or biosensors. Oligonucleotide probes are single-stranded nucleic acid fragments that can be tailored to have high specificity and affinity for different targets including nucleic acids, proteins, small molecules, and ions. One can divide oligonucleotide-based probes into two main categories: hybridization probes that are based on the formation of complementary base-pairs, and aptamer probes that exploit selective recognition of nonnucleic acid analytes and may be compared with immunosensors. Design and construction of hybridization and aptamer probes are similar. Typically, oligonucleotide (DNA, RNA) with predefined base sequence and length is modified by covalent attachment of reporter groups (one or more fluorophores in fluorescence-based probes). The fluorescent labels act as transducers that transform biorecognition (hybridization, ligand binding) into a fluorescence signal. Fluorescent labels have several advantages, for example high sensitivity and multiple transduction approaches (fluorescence quenching or enhancement, fluorescence anisotropy, fluorescence lifetime, fluorescence resonance energy transfer (FRET), and excimer-monomer light switching). These multiple signaling options combined with the design flexibility of the recognition element (DNA, RNA, PNA, LNA) and various labeling strategies contribute to development of numerous selective and sensitive bioassays. This review covers fundamentals of the design and engineering of oligonucleotide probes, describes typical construction approaches, and discusses examples of probes used both in hybridization studies and in aptamer-based assays.     

Sensitivity by combination: immuno-PCR and related technologies

The versatility of immunoassays for the detection of antigens can be combined with the signal amplification power of nucleic acid amplification techniques in a broad range of innovative detection strategies. This review summarizes the spectrum of both, DNA-modification techniques used for assay enhancement and the resulting key applications. In particular, it focuses on the highly sensitive immuno-PCR (IPCR) method. This technique is based on chimeric conjugates of specific antibodies and nucleic acid molecules, the latter of which are used as markers to be amplified by PCR or related techniques for signal generation and read-out. Various strategies for the combination of antigen detection and nucleic acid amplification are discussed with regard to their laboratory analytic performance, including novel approaches to the conjugation of antibodies with DNA, and alternative pathways for signal amplification and detection. A critical assessment of advantages and drawbacks of these methods for a number of applications in clinical diagnostics and research is conducted. The examples include the detection of viral and bacterial antigens, tumor markers, toxins, pathogens, cytokines and other targets in different biological sample materials.     

Amplified Self‐Immolative Release of Small Molecules by Spatial Isolation of Reactive Groups on DNA‐Minimal Architectures

Triggering the release of small molecules in response to unique biomarkers is important for applications in drug delivery and biodetection. Due to low quantities of biomarker, amplifying release is necessary to gain appreciable responses. Nucleic acids have been used for both their biomarker‐recognition properties and as stimuli, notably in amplified small‐molecule release by nucleic‐acid‐templated catalysis (NATC). The multiple components and reversibility of NATC, however, make it difficult to apply in vivo. Herein, we report the use of the hybridization chain reaction (HCR) for the amplified, conditional release of small molecules from standalone nanodevices. We couple HCR with a DNA‐templated reaction resulting in the amplified, immolative release of small molecules. We integrate the HCR components into single nanodevices as DNA tracks and spherical nucleic acids, spatially isolating reactive groups until triggering. This could be applied to biosensing, imaging, and drug delivery.     

Application and analysis of structure-switching aptamers for small molecule quantification

Modern tools for the analysis of cellular function aim for the quantitative measurement of all members of a given class of biological molecules. Of the analyte classes, nucleic acid measurements are typically the most tractable, both on an individual analyte basis and in parallel. Thus, tools are being sought to enable measurement of other cellular molecules using nucleic acid biosensors. Of the variety of potential nucleic acid biosensor strategies, structure-switching aptamers (SSAs) present a unique opportunity to couple sensing and readout of the target molecule. However, little has been characterized about the parameters that determine the fidelity of the signal from SSA biosensors. In this study, a small molecule biosensor based on a SSA was engineered to detect the model small molecule, theophylline, in solution. Quantitative theophylline detection over nearly three orders-of-magnitude was achieved by scintillation counting and quantitative PCR. Further analysis showed that the biosensor fidelity is primarily controlled by the relative stability of the two conformations of the SSA.     

DNA/银纳米簇在分析检测中的应用

银纳米簇(AgNCs)为几个到数十个原子所组成的聚集体,核尺寸小于2 nm,具有优异的物理化学性质,常以聚合物、蛋白质、DNA等作为模板采用化学合成法制备,其中以DNA为模板合成的AgNCs(DNA/AgNCs)是一种新型的发光纳米材料,其突出的荧光特性和良好的生物相容性,被应用于纳米传感器、细胞标记与检测等多种分析领...     

Recent progress in graphene-material-based optical sensors

Graphene material has been widely used for optical sensors owing to its excellent properties, including high-energy transfer efficiency, large surface area, and great biocompatibility. Different analytes such as nucleic acids, proteins, and small molecules can be detected by graphene-material-based optical sensors. This review provides a comprehensive discussion of graphene-material-based optical sensors focusing on detection mechanisms and biosensor designs. Challenges and future perspectives for graphene-material-based optical sensors are also presented.     

Amplified label-free electrical detection of DNA hybridization

A new protocol is described for amplifying label-free electrochemical measurements of DNA hybridization based on the enhanced accumulation of purine nucleobases in the presence of copper ions . Such electrical DNA assays involve hybridization of the target to inosine-substituted oligonucleotide probes (captured on magnetic beads), acidic dipurinization of the hybrid DNA, and adsorptive chronopotentiometric stripping measurements of the free nucleobases in the presence of copper ions. Both amplified adenine and guanine peaks can be used for detecting the DNA hybridization. The dramatic signal amplification advantage of this type of detection has been combined with efficient magnetic removal of non-complementary DNA, use of microliter sample volumes and disposable transducers. Factors influencing the signal enhancement were assessed and optimized. A detection limit of 40 fmol (250 pg) was obtained with 10 min hybridization and 5 min adsorptive-accumulation times. The advantages of this procedure were demonstrated by its application in the detection of DNA segments related to the BRCA1 breast cancer gene. The copper enhancement holds great promise not only for the detection of DNA hybridization, but also for trace measurement of nucleic acids.     

Electrokinetic techniques applied to electrochemical DNA biosensors

Electrokinetic techniques are contact-free methods currently used in many applications, where precise handling of biological entities, such as cells, bacteria or nucleic acids, is needed. These techniques are based on the effect of electric fields on molecules suspended in a fluid, and the corresponding induced motion, which can be tuned according to some known physical laws and observed behaviours. Increasing interest on the application of such strategies in order to improve the detection of DNA strands has appeared during the recent decades. Classical electrode-based DNA electrochemical biosensors with combined electrokinetic techniques present the advantage of being able to improve the working electrode's bioactive part during their fabrication and also the hybridization yield during the sensor detection phase. This can be achieved by selectively manipulating, driving and directing the molecules towards the electrodes increasing the speed and yield of the floating DNA strands attached to them. On the other hand, this technique can be also used in order to make biosensors reusable, or reconfigurable, by simply inverting its working principle and pulling DNA strands away from the electrodes. Finally, the combination of these techniques with nanostructures, such as nanopores or nanochannels, has recently boosted the appearance of new types of electrochemical sensors that exploit the time-varying position of DNA strands in order to continuously scan these molecules and to detect their properties. This review gives an insight into the main forces involved in DNA electrokinetics and discusses the state of the art and uses of these techniques in recent years.     

Review: Carbon nanotube based electrochemical sensors for biomolecules

Carbon nanotubes (CNTs) have been incorporated in electrochemical sensors to decrease overpotential and improve sensitivity. In this review, we focus on recent literature that describes how CNT-based electrochemical sensors are being developed to detect neurotransmitters, proteins, small molecules such as glucose, and DNA. Different types of electrochemical methods are used in these sensors including direct electrochemical detection with amperometry or voltammetry, indirect detection of an oxidation product using enzyme sensors, and detection of conductivity changes using CNT-field effect transistors (FETs). Future challenges for the field include miniaturizing sensors, developing methods to use only a specific nanotube allotrope, and simplifying manufacturing.     

Single-molecule studies on DNA and RNA.

DNA and RNA are the most individual molecules known. Therefore, single-molecule experiments with these nucleic acids are particularly useful. This review reports on recent experiments with single DNA and RNA molecules. First, techniques for their preparation and handling are summarised including the use of AFM nanotips and optical or magnetic tweezers. As important detection techniques, conventional and near-field microscopy as well as fluorescence resonance energy transfer (FRET) and fluorescence correlation spectroscopy (FCS) are touched on briefly. The use of single-molecule techniques currently includes force measurements in stretched nucleic acids and in their complexes with binding partners, particularly proteins, and the analysis of DNA by restriction mapping, fragment sizing and single-molecule hybridisation. Also, the reactions of RNA polymerases and enzymes involved in DNA replication and repair are dealt with in some detail, followed by a discussion of the transport of individual nucleic acid molecules during the readout and use of genetic information and during the infection of cells by viruses. The final sections show how the enormous addressability in nucleic acid molecules can be exploited to construct a single-molecule field-effect transistor and a walking single-molecule robot, and how individual DNA molecules can be used to assemble a single-molecule DNA computer.     

光电化学传感器的研究进展

光电化学传感器以光作为激发源,以光电流或光电压作为检测信号,具有响应快速、灵敏度高、设备简单等特点,目前已在环境、食品、医学等多个领域的分析测试中得到广泛应用。该文阐述了光电转换材料与光电化学传感器的制备方法,介绍了光电化学传感器的原理和分类。光电化学传感器包含光寻址电位型传感器和电流型光电化学传感器,其中,电流型光电化学传感器由于优良的光电性能、检出限低、所需材料低廉且易加工等优势而被广泛应用。文中着重介绍了电流型光电化学传感器在金属离子、有机污染物、核酸、蛋白质、细胞等方面的应用,并对光电化学传感器的发展前景进行了展望。     

Amplified Self-Immolative Release of Small Molecules by Spatial Isolation of Reactive Groups on DNA-Minimal Architectures

Triggering the release of small molecules in response to unique biomarkers is important for applications in drug delivery and biodetection. Due to low quantities of biomarker, amplifying release is necessary to gain appreciable responses. Nucleic acids have been used for both their biomarker-recognition properties and as stimuli, notably in amplified small-molecule release by nucleic-acid-templated catalysis (NATC). The multiple components and reversibility of NATC, however, make it difficult to apply in vivo. Herein, we report the use of the hybridization chain reaction (HCR) for the amplified, conditional release of small molecules from standalone nanodevices. We couple HCR with a DNA-templated reaction resulting in the amplified, immolative release of small molecules. We integrate the HCR components into single nanodevices as DNA tracks and spherical nucleic acids, spatially isolating reactive groups until triggering. This could be applied to biosensing, imaging, and drug delivery.     

化学发光在生化分析中的应用研究进展

化学发光分析是利用化学发光反应的发光现象,对化学发光物质由激发态跃迁回基态时发出的光信号进行测量的一种分析方法。化学发光分析具有无需外来光源、灵敏度高、操作方便、分析快速以及易于实现自动化等优点,可与其它分析技术联用,在临床检验、药物分析和环境监测等领域具有广泛应用。近年来,纳米材料、生物芯片及微流控技术的引入促进了化学发光分析技术的发展。本文综述了化学发光分析与高效液相色谱、毛细管电泳、量子点、微流控芯片和微阵列、以及滚环扩增、等温指数扩增和两级等温扩增联用技术的发展,介绍了化学发光分析技术在DNA、生物小分子、生物酶、蛋白质和金属离子检测中的应用研究进展,并展望了其发展趋势。